Cargando…

Proteomic variations of esophageal squamous cell carcinoma revealed by combining RNA-seq proteogenomics and G-PTM search strategy

BACKGROUND: Cancer that arises from epithelial cells of the esophagus is called esophagus squamous cell carcinoma (ESCC) and is mostly observed in developing nations. Evaluation of cancer genomes and its regulation into proteins plays a predominant role in understanding the cancer progressions. Mass...

Descripción completa

Detalles Bibliográficos
Autores principales:	Ramesh, Pooja, Nagarajan, Vidhyavathy, Khanchandani, Vartika, Desai, Vasanth Kumar, Niranjan, Vidya
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Elsevier 2020
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7472856/ https://www.ncbi.nlm.nih.gov/pubmed/32913912 http://dx.doi.org/10.1016/j.heliyon.2020.e04813

Ejemplares similares

Integration of exome-seq and mRNA-seq using DawnRank, identified genes involved in innate immunity as drivers of breast cancer in the Indian cohort
por: Nirgude, Snehal, et al.
Publicado: (2023)

Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy
por: Cesnik, Anthony J., et al.
Publicado: (2015)

qPTM: an updated database for PTM dynamics in human, mouse, rat and yeast
por: Yu, Kai, et al.
Publicado: (2022)

Decoding the PTM-switchboard of Notch
por: Antfolk, Daniel, et al.
Publicado: (2019)

Integrative proteogenomic characterization of early esophageal cancer
por: Li, Lingling, et al.
Publicado: (2023)

Bioinformatic and Proteomic Analysis of Bulk Histones Reveals PTM Crosstalk and Chromatin Features
por: Zhang, Chunchao, et al.
Publicado: (2014)

MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics
por: Polasky, Daniel A., et al.
Publicado: (2023)

Utilizing Optimized Tools to Investigate PTM Crosstalk: Identifying Potential PTM Crosstalk of Acetylated Mitochondrial Proteins
por: Horita, Henrick, et al.
Publicado: (2018)

Breast cancer quantitative proteome and proteogenomic landscape
por: Johansson, Henrik J., et al.
Publicado: (2019)

Proteogenomic landscape of squamous cell lung cancer
por: Stewart, Paul A., et al.
Publicado: (2019)

PTMphinder: an R package for PTM site localization and motif extraction from proteomic datasets
por: Wozniak, Jacob M., et al.
Publicado: (2019)

Proteomic and molecular dynamic investigations of PTM-induced structural fluctuations in breast and ovarian cancer
por: Tikhonov, Dmitry, et al.
Publicado: (2021)

topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins
por: Su, Min-Gang, et al.
Publicado: (2014)

Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection
por: Salz, Renee, et al.
Publicado: (2021)

Cells, shared memory and breaking the PTM code
por: Creixell, Pau, et al.
Publicado: (2012)

FAIMS Enhances the Detection of PTM Crosstalk Sites
por: Adoni, Kish R., et al.
Publicado: (2022)

PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results
por: Geiszler, Daniel J., et al.
Publicado: (2020)

MSstatsPTM: Statistical Relative Quantification of Posttranslational Modifications in Bottom-Up Mass Spectrometry-Based Proteomics
por: Kohler, Devon, et al.
Publicado: (2022)

Proteomics analysis and proteogenomic characterization of different physiopathological human lenses
por: Wu, Xiaohang, et al.
Publicado: (2017)

Deciphering the PTM codes of the tumor suppressor p53
por: Wen, Jia, et al.
Publicado: (2021)

Quantitative profiling of PTM stoichiometry by resolvable mass tags
por: Chen, Ying, et al.
Publicado: (2022)

Complementary PTM Profiling of Drug Response in Human Gastric Carcinoma by Immunoaffinity and IMAC Methods with Total Proteome Analysis
por: Stokes, Matthew P., et al.
Publicado: (2015)

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease
por: Torres, Matthew P., et al.
Publicado: (2016)

OryzaPG-DB: Rice Proteome Database based on Shotgun Proteogenomics
por: Helmy, Mohamed, et al.
Publicado: (2011)

A sample preparation workflow for adipose tissue shotgun proteomics and proteogenomics
por: Khudyakov, Jane I., et al.
Publicado: (2018)

dbPTM: an information repository of protein post-translational modification
por: Lee, Tzong-Yi, et al.
Publicado: (2006)

Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer
por: Song, Ehwang, et al.
Publicado: (2017)

Unraveling the small proteome of the plant symbiont Sinorhizobium meliloti by ribosome profiling and proteogenomics
por: Hadjeras, Lydia, et al.
Publicado: (2023)

The Proteogenomic Mapping Tool
por: Sanders, William S, et al.
Publicado: (2011)

The bacterial proteogenomic pipeline
por: Uszkoreit, Julian, et al.
Publicado: (2014)

Proteogenomic characterization of cholangiocarcinoma
por: Deng, Mengjie, et al.
Publicado: (2023)

Identification of Conomarphin Variants in the Conus eburneus Venom and the Effect of Sequence and PTM Variations on Conomarphin Conformations
por: Itang, Corazon Ericka Mae M., et al.
Publicado: (2020)

The Integration of Proteome-Wide PTM Data with Protein Structural and Sequence Features Identifies Phosphorylations that Mediate 14-3-3 Interactions
por: Egbert, C. M., et al.
Publicado: (2023)

Networking of predicted post-translational modification (PTM) sites in human EGFR
por: Malik, Arshi, et al.
Publicado: (2019)

The Burden of Post-Translational Modification (PTM)—Disrupting Mutations in the Tumor Matrisome
por: Holstein, Elisa, et al.
Publicado: (2021)

PTMint database of experimentally verified PTM regulation on protein–protein interaction
por: Hong, Xiaokun, et al.
Publicado: (2022)

Addressing Statistical Biases in Nucleotide-Derived Protein Databases for Proteogenomic Search Strategies
por: Blakeley, Paul, et al.
Publicado: (2012)

Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification
por: Li, Honglan, et al.
Publicado: (2016)

Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics
por: Verbruggen, Steven, et al.
Publicado: (2021)

Proteogenomic analysis of the total and surface-exposed proteomes of Plasmodium vivax salivary gland sporozoites
por: Swearingen, Kristian E., et al.
Publicado: (2017)

Cannot write session to /tmp/vufind_sessions/sess_oq9betlvd5qonp1o2jo6ehgb9t